De novo identification of viral pathogens from cell culture hologenomes
IR@IGIB: CSIR-Institute of Genomics & Integrative Biology, New Delhi
View Archive Info| Field | Value | |
| Title |
De novo identification of viral pathogens from
cell culture hologenomes
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| Creator |
Patowary , Ashok
Chauhan, Rajendra Kumar Singh, Meghna Vellarikkal, Shamsudheen K Periwal, Vinita P , K Kushwaha Sapkal , N Gajanan Bondre, Vijay P Gore, Milind M Sivasubbu, Sridhar Scaria, Vinod |
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| Subject |
CH1 Chemical Biology
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| Description |
Abstract
Background
Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak
response system, especially in the case of emerging infectious diseases and viral epidemics. This
process is generally tedious and time-consuming thus making it ineffective in traditional settings.
The added complexity in these situations is the non-availability of pure isolates of pathogens as
they are present as mixed genomes or hologenomes. Next-generation sequencing approaches
offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and
affordable costs, apart from making it possible to decipher complex interactions between
genomes at a scale that was not possible before. The widespread application of next-generation
sequencing in this field has been limited by the non-availability of an efficient computational
pipeline to systematically analyze data to delineate pathogen genomes from mixed population of
genomes or hologenomes.
Findings
We applied next-generation sequencing on a sample containing mixed population of genomes
from an epidemic with appropriate processing and enrichment. The data was analyzed using an
extensive computational pipeline involving mapping to reference genome sets and de-novo
assembly. In depth analysis of the data generated revealed the presence of sequences
corresponding to Japanese encephalitis virus. The genome of the virus was also independently
de-novo assembled. The presence of the virus was in addition, verified using standard molecular
biology techniques.
Conclusions
Our approach can accurately identify causative pathogens from cell culture hologenome samples
containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to
identify and isolate pathogen genomes and understand their genomic variability during
outbreaks.
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://openaccess.igib.res.in/158/1/Patowary%20et%20al%202012_JEHologenomics.pdf
Patowary , Ashok and Chauhan, Rajendra Kumar and Singh, Meghna and Vellarikkal, Shamsudheen K and Periwal, Vinita and P , K Kushwaha and Sapkal , N Gajanan and Bondre, Vijay P and Gore, Milind M and Sivasubbu, Sridhar and Scaria, Vinod De novo identification of viral pathogens from cell culture hologenomes. De novo identification of viral pathogens from cell culture hologenomes . |
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| Relation |
http://openaccess.igib.res.in/158/
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